[T-Mobile Samsung Galaxy S II SGH-T989] bmg002:
none of those folders are your "live" init.d folder, those are all backups from apps that modify your init.d folder. Your live init.d folder is hiding at /system/etc/init.d

This folder is mounted as read-only by default to prevent users from mucking it up. So IF you want to play in that folder, I would first do a nandroid (it is safe to assume any "read only" folder has stuff in it that android or a dev doesn't want you playing with in order to prevent you from screwing things up... nandroid allows you to recover if you screw something up), make a backup of the init.d folder (never hurts to have a backup... have it either on your phone or on your PC or both... I did both), then remount the /system drive as rw and play away. I just removed the scripts (after reading them) that seemed to set things that conflicted with what I had set in performance control (or other similar apps like rom toolbox ro trickster mod) or ones that made changes I didn't want/need (like disabling logcat). And since I was more concerned with quick boot times than 100% optimized performance of my phone, I turned off zipalign and db optimizations and the cron jobs... I can run those manually if I feel the need to run them.

BUT if you tweak these and start getting rr's, sod's, fc's, etc, I imagine most people will tell you to clean-flash to verify that the problems you are having are actually ROM/Kernel related and not related to tweaks that you did. If you play with a read-only folder, chances are you are changing something that the ROM or Kernel setup at install time.

If things go bad and you don't have a nandroid or can't get in to repair the init.d folder, you can always get it back by re-flashing the ROM. This is one folder that the ROM overwrites. So if you tweak these scripts or remove them, back up the folder onto your PC BEFORE flashing your ROM so you can put it back afterwards.

EDIT: I would also read through the script before deleting it. If you can't make out what it is doing, research what it does before deleting it. I do not believe any init.d script is CRITICAL to keeping your phone running, but at the same time the dev of the ROM put them in there for a reason...

EDIT2: I have a new problem now: I can't get adb to work. Is anybody else having issues with adb running Cl3Kener's build? Mass_Storage is also no longer an option. Do both of these work in the nightlies or for others on Cl3Kener's build (which would mean I had a bad flash)?

EDIT3: adb now works (after not really doing anything) and I can get mass storage to work by setting sys.usb.config to "acm,mass_storage,adb"... (which to me looks like it is mostly just changing the idVendor value, but I could be wrong), but I can't actually "mount" the new drives in windows... must be something I am missing... any tips?

EDIT4: man that is a lot of edits... but got it all working (mass_storage)... it isn't pretty... it is using shell scripts to modify files so it is quite messy, but mass storage is working (after running the script) and adb is working (without any tweaking). Hopefully this gets fixed in a future release.

I can pass off the info if anybody else is like me and wants mass_storage working now, but I do NOT know if my scripts are going to work for every device, so I will more just be providing info on how to write the script yourself (I don't want to be responsible for when somebody bricks their phone due to mounting the wrong partition).